Selecting SRM targets

Who are the lucky winners?

Now that I have a full Skyline document, I can select proteins I want to use for a Selected Reaction Monitoring assay. I’m going to pick proteins that are candidate biomarkers, either because they show clear patterns of variation between experimental conditions, or because they are ecologically significant.

Step 1: Reimport data files

After Laura posted this issue, I realized I imported my raw files into Skyline instead of my demultiplexed files. Before I could proceed with any analyses, I had to replace the raw files with demultiplexed ones.

Step 2: Remove files with no data

If you look at the top right corner of my Skyline document, you’ll see there are files with no data (no associated histograms).

Samples 17, 21, 22 and 23 produced no data in the Skyline document. They also weren’t included in the full .blib. I checked the mass spectrometery sequence file and found that oyster 21 was my blank (so there should be no data in it!) and oyster 17, 22 and 23 corresponded with my original 0107 sample.